Wednesday, February 16, 2011

An acronym in cheminformatics: SSAM for state and shape annotation marker

SSAM stands for state and shape annotation marker. AN SSAM is a pair of two lowercase letters that mark the beginning of a component annotation in a CurlySMILES notation [1,2].
SSAM-annotations specify chemical compounds and complex materials by features such as physical state and nanostructure type. The following notation with two SSAM annotations, encoding a two-dimensional grain of a graphene atomic patchwork [3], illustrates the annotation format:


The SMILES notation [C] represents carbon in SQC. The first annotation starts with SSAM al defining an atomic layer followed by the annotation dictionary entry which specifies the carbon allotrope graphene. The second annotation describes the 2D-grain, using gr as SSAM.

[1] Axel Drefahl: CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures. Journal of Cheminformatics 2011, 3:1.
DOI: 10.1186/1758-2946-3-1.
[2] Axel Drefahl: CurlySMILES: state and shape annotations [].
P. Y. Huang, C. S. Ruiz-Vargas, A. M. van der Zande, W. S. Whitney, M. P. Levendorf, J. W. Keyek, S. Garg, J. S. Alden, C. J. Hustedt, Ye Zhu, J. Park, P. L. McEuen and D. A. Muller: Grains and grain boundaries in sinle-layer graphene atomic patchwork quilts. Nature 2011, 469 (7330), pp. 389-392. DOI: 10.1038/nature09718.

No comments:

Post a Comment